Lifeboat Foundation

Scientists at the University of California, San Francisco (UCSF) and IBM Research have created a virtual library of thousands of “command sentences” for cells using machine learning. These “sentences” are based on combinations of “words” that direct engineered immune cells to find and continuously eliminate cancer cells.

This research, which was recently published in the journal Science, is the first time that advanced computational techniques have been applied to a field that has traditionally progressed through trial-and-error experimentation and the use of pre-existing molecules rather than synthetic ones to engineer cells.

The advance allows scientists to predict which elements – natural or synthesized – they should include in a cell to give it the precise behaviors required to respond effectively to complex diseases.

On the journey from gene to protein, a nascent RNA molecule can be cut and joined, or spliced, in different ways before being translated into a protein. This process, known as alternative splicing, allows a single gene to encode several different proteins. Alternative splicing occurs in many biological processes, like when stem cells mature into tissue-specific cells. In the context of disease, however, alternative splicing can be dysregulated. Therefore, it is important to examine the transcriptome—that is, all the RNA molecules that might stem from genes—to understand the root cause of a condition.

However, historically it has been difficult to “read” RNA molecules in their entirety because they are usually thousands of bases long. Instead, researchers have relied on so-called short-read RNA sequencing, which breaks RNA molecules and sequence them in much shorter pieces—somewhere between 200 to 600 bases, depending on the platform and protocol. Computer programs are then used to reconstruct the full sequences of RNA molecules.

Short-read RNA sequencing can give highly accurate sequencing data, with a low per-base error rate of approximately 0.1% (meaning one base is incorrectly determined for every 1,000 bases sequenced). Nevertheless, it is limited in the information that it can provide due to the short length of the sequencing reads. In many ways, short-read RNA sequencing is like breaking a large picture into many jigsaw pieces that are all the same shape and size and then trying to piece the picture back together.

Novel drugs, such as vaccines against COVID-19, among others, are based on drug transport using nanoparticles. Whether this drug transport is negatively influenced by an accumulation of blood proteins on the nanoparticle’s surface was not clarified for a long time.

Scientists at the Max Planck Institute for Polymer Research have now followed the path of such a particle into a cell using a combination of several microscopy methods. They were able to observe a cell-internal process that effectively separates blood components and nanoparticles.

Nanoparticles are a current field of research and it is impossible to imagine modern medicine without them. They serve as microscopic drug capsules that are less than a thousandth of a millimeter in diameter. Among other things, they are used in current vaccines against COVID-19 to effectively deliver active ingredients to where they are actually needed. In most cases, the capsules dock onto cells, are enveloped by them, and are absorbed into them. Inside the cell, chemical processes can then open the capsules, releasing the active ingredient.

Metastasisation — the spreading of cancer cells from the primary tumour into surrounding body tissues and organs — is the leading cause of death in cancer patients. Now a new study has found a potential way to stop these cancer cells from entering a person’s blood. Scientists from Israel are working to produce the world’s first preventative drug to help stop tumours that cause secondary cancer, as reported byThe Times of Israel.

University of Queensland researchers have identified a pathway in cells that could be used to reprogram the body’s immune system to fight back against both chronic inflammatory and infectious diseases.

Dr. Kaustav Das Gupta and Professor Matt Sweet from UQ’s Institute for Molecular Bioscience discovered that a molecule derived from glucose in immune cells can both stop bacteria growing and dampen inflammatory responses. Dr. Das Gupta said that the finding is a critical step towards future therapeutics that train immune cells.

The research was published in Proceedings of the National Academy of Sciences (PNAS).

See the people building up Atlas.

How does Atlas recognize and interact with objects? How do we develop new Atlas behaviors? Why is manipulation important for the future of robotics?

Continue reading “Inside the Lab: Taking Atlas From Sim to Scaffold” »

A new study has identified a promising drug candidate that can protect neurons from degeneration in mouse models of Parkinson’s disease. The research is published in Science Translational Medicine.

Addressing an unmet need

Parkinson’s disease (PD) is the second most common neurodegenerative disease, and over the last 25 years, the prevalence of PD has doubled, presenting a large health burden across the globe.

— Two papers show that large language models, including ChatGPT, can pass the USMLE.

The ultraviolet nail polish drying devices used to cure gel manicures may pose more of a public health concern than previously thought. Researchers at the University of California San Diego studied these ultraviolet (UV) light emitting devices, and found that their use leads to cell death and cancer-causing mutations in human cells.

The devices are a common fixture in nail salons, and generally use a particular spectrum of UV light (340-395nm) to cure the chemicals used in gel manicures. While tanning beds use a different spectrum of UV light (280-400nm) that studies have conclusively proven to be carcinogenic, the spectrum used in the nail dryers has not been well studied.

“If you look at the way these devices are presented, they are marketed as safe, with nothing to be concerned about,” said Ludmil Alexandrov, a professor of bioengineering as well as cellular and molecular medicine at UC San Diego, and corresponding author of the study published Jan. 17 in Nature Communications. “But to the best of our knowledge, no one has actually studied these devices and how they affect human cells at the molecular and cellular levels until now.”